Targeted Haplotype Comparisons between South African Wheat Cultivars Appear Predictive of Pre-harvest Sprouting Tolerance.

Scott L Sydenham,Annelie Barnard

doi:10.3389/fpls.2018.00063

Scott L Sydenham, Annelie Barnard

Open Access

https://doi.org/10.3389/fpls.2018.00063

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Abstract

Pre-harvest sprouting (PHS) has been a serious production constraint for over two decades, especially in the summer rainfall wheat production regions of South Africa. It is a complex genetic trait controlled by multiple genes, which are significantly influenced by environmental conditions. This complicates the accurate prediction of a cultivar's stability in terms of PHS tolerance. A number of reports have documented the presence of major QTL on chromosomes 3A and 4A of modern bread wheat cultivars, which confer PHS tolerance. In this study, the SSR marker haplotype combination of chromosomes 3A and 4A of former and current South African cultivars were compared with the aim to select for improved PHS tolerance levels in future cultivars. A total of 101 wheat cultivars, including a susceptible cultivar and five international tolerant sources, were used in this study. These cultivars and donors were evaluated for their PHS tolerance by making use of a rain simulator. In addition, five seeds of each entry were planted out into seedling trays and leaf material harvested for DNA isolation. A modified CTAB extraction method was used before progressing to downstream PCR applications. Eight SSR markers targeted from the well-characterized 3A and 4A QTL regions associated with PHS tolerance, were used to conduct targeted haplotype analysis. Additionally, recently published KASP SNP markers, which identify the casual SNP mutations within the TaPHS1 gene, were used to genotype the germplasm. The haplotype marker data and phenotypic PHS data were compared across all cultivars and different production regions. A relative change in observed phenotypic variation percentage was obtained per marker allele and across marker haplotype combinations when compared to the PHS susceptible cultivar, Tugela-DN. Clear favorable haplotypes, contributing 40–60% of the variation for PHS tolerance, were identified for QTL 3A and 4A. Initial analyses show haplotype data appear to be predictive of PHS tolerance status and germplasm can now be selected to improve PHS tolerance. These haplotype data are the first of its kind for PHS genotyping in South Africa. In future, this can be used as a tool to predict the possible PHS tolerance range of a new cultivar.

Highlights

Pre-harvest sprouting (PHS) is a common phenomenon in the wheat (Triticum aestivum L.) producing areas of South Africa and has been well-documented over the past two decades (Barnard et al, 1997; Barnard, 2001; Barnard and Bona, 2004; Barnard and Smith, 2009)
All wheat cultivars grown in South Africa are red wheat types with exceptional bread making quality characteristics (Smit et al, 2010)
It is wellknown that environmental conditions during grain filling can have a large effect on the expression of dormancy (Biddulph et al, 2007)

Summary

Introduction

Pre-harvest sprouting (PHS) is a common phenomenon in the wheat (Triticum aestivum L.) producing areas of South Africa and has been well-documented over the past two decades (Barnard et al, 1997; Barnard, 2001; Barnard and Bona, 2004; Barnard and Smith, 2009). The PHS tolerance levels in South African wheat cultivars has improved significantly over the years as a result of successful breeding (Smit et al, 2010) These winter wheat cultivars can be categorized into three major groups, namely cultivars that are highly tolerant to PHS, cultivars that are highly susceptible to PHS and a third moderate group that includes cultivars that are strongly influenced by the environment (Barnard and Smith, 2009). Drought conditions combined with high temperatures during grain filling, tend to increase dormancy in wheat (Mares and Mrva, 2014)

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